DOCSLIB.ORG

1 Insights Into Transporter Classifications: an Outline Of

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
1 Insights Into Transporter Classifications: an Outline Of 1 1 Insights into Transporter Classifications: an Outline of Transporters as Drug Targets Michael Viereck,1 Anna Gaulton,2 and Daniela Digles1 1University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria 2EMBL – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK 1.1 Introduction Classifications are a useful tool to get an overview of a topic. They show instan- ces grouped together that share common properties according to the creator of the classification, and as in the case of hierarchical classifications, they allow to draw conclusions on the relation of different classes. In the case of the identifica- tion of drug targets (including transporters as the main drug target), several pub- lications show classifications as a helpful tool. Imming et al. [1] categorized drugs according to their targets, to get an esti- mate on the number of known drug targets, including channels and transporters. Drugs on the market were connected to a target only if it was described as the main target in the literature. For transport proteins (including uniporters, sym- porters, and antiporters), this identified six different types of transporter groups that are relevant as drug targets. These are the cation-chloride cotransporter + + + + (CCC) family (SLC 12), Na /H antiporters (SLC 9), proton pumps, Na /K ATPases, the eukaryotic (putative) sterol transporter (EST) family, and the neu- + rotransmitter/Na symporter (NSS) family (SLC 6). These families mainly belong to either ATPases or solute carriers (SLC). Whether the EST family is treated as transport protein or not depends on the classification used. Rask-Andersen et al. [2] used a manually curated and extended version of the DrugBank [3] data from 2009 to analyze drug targets. They identified 435 thera- peutic effect-mediating targets, where the third largest group (67) is of trans- porter proteins (including 35 ion channels). These transport proteins are mainly targeted by antihypertensive drugs, diuretics, anaesthetics, and antiarrhythmic drugs. In a more recent study [4], they analyzed the Drugs in the Clinical Trials Database by CenterWatch to investigate the targets of new drug candidates. Transporters as Drug Targets, First Edition. Edited by Gerhard F. Ecker, Rasmus P. Clausen, and Harald H. Sitte. 2017 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2017 by Wiley-VCH Verlag GmbH & Co. KGaA. 2 1 Insights into Transporter Classifications: an Outline of Transporters as Drug Targets Transporter proteins in this data set were classified using the transporter classifi- cation (TC) system established by Saier et al. [5]. This chapter will first give an overview on selected existing transporter classifi- cations and then describe our process of creating a combined classification scheme for the ChEMBL [6] database. Finally, the investigation of the counts of drugs and diseases for one example protein superfamily is provided, to show the usefulness of classifications in characterizing related proteins and to give a first overview on the topic of this book, focusing on transporters as drug targets. 1.2 Available Transporter Classifications As a consequence of the significance of the transport process for every living organism, already numerous classification schemes for membrane transport pro- teins of several organisms exist. Quite a few focus only on specific families, for instance, the SLC superfamily or the ABC transporter superfamily. Table 1.1 shows a selection of membrane transport protein databases with a focus on human proteins. To keep the table concise, databases focusing on different orga- nisms (e.g., the plant membrane protein database Aramemnon [7], the yeast transport protein database YTPdb [8], or ABCdb [9], a database about bacterial ABC systems) are not included, even though bacterial or protozoal channels and transporters can also be promising drug targets [10,11]. We were interested in classification schemes that not only try to cover the full variety of human membrane transport proteins but also provide their own com- plete classification. Therefore, we analyzed the functional and phylogenetic clas- sification scheme of the Transporter Classification Database (TCDB), the more pharmacology-driven IUPHAR/BPS classification, and the mainly functional- driven classification of channels and transporters in the bioactivity database ChEMBL-16 [18]. These were recently reviewed in [19], which provides a more detailed discussion for the interested reader. In addition, we included the SLC series [12], which is a well-known nomenclature system. 1.2.1 TCDB The transporter classification system developed in the laboratory of Saier is to some extent comparable to the Enzyme Commission (EC) classification. But while the EC system concentrates on the function of enzymes, the transporters in the TC system are classified according to function and phylogeny [20]. Both schemes are recommended by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology [21,22] (URL: http://www.chem .qmul.ac.uk/iubmb/mtp/). The TC is also included in several other databases such as UniProt [23] (URL: www.UniProt.org/) or the Protein Data Bank (PDB) [24] (URL: http://www.rcsb.org/pdb/). TCDB is an exhaustive classification Table 1.1 Selection of transporter collections with a focus on human membrane transport proteins. Database Description URL Included proteins Limited to organisms Bioparadigms SLC Online resource of the 52 human slc.bioparadigms.org/ Solute carriers Homo sapiens Series [12] solute carrier families ChEMBL [6] Large-scale bioactivity database for https://www.ebi.ac.uk/chembldb/target/ Proteins with bio- — drug discovery browser activity data Human ABC Basic information about human www.nutrigene.4t.com/humanabc.htm ABC transporters Homo sapiens transporters [13] ABC transporters IUPHAR/BPS Guide to Overview of human drug targets www.guidetopharmacology.org Drug targets Homo sapiens, and PHARMACOLOGY [14] with their pharmacology Mus musculus, Rattus norvegicus TCDB [5] Provides a classification scheme www.tcdb.org/ Channels, transport- — for all membrane transport pro- ers, auxiliary trans- teins in all living organism port proteins TransportDB [15] Genomic comparison of mem- www.membranetransport.org/index.html Channels, transport- Complete genome- brane transport proteins, predic- ers, auxiliary trans- sequenced organisms 1.2 Available Transporter Classi tion of their function, and port proteins (365 total) classification according to TCDB Transporter substrate Provides a transporter substrate http://tsdb.cbi.pku.edu.cn/home.cgi Transporters — database (TSdb) [16] repository with mappings to KEGG pathways UCSF-FDA Provides information on transport- http://bts.ucsf.edu/fdatransportal/ Transporters Homo sapiens TransPortal [17] ers important in the drug discov- ery process fi cations 3 4 1 Insights into Transporter Classifications: an Outline of Transporters as Drug Targets including over 750 transporter families, and over 10 000 protein sequences are included in the Transporter Classification Database [5] (URL: www.tcdb.org/). The database stores sequences and information regarding all classified transport proteins. Transporters can be found in the database either by browsing the clas- sification or by directly searching for the protein of interest (e.g., by UniProt accession number). For unclassified proteins, similar sequences can be found using a BLAST search. The classification scheme contains five levels as exemplified for 2.A.22.6.3 in Table 1.2. The first level number indicates the class of membrane transport pro- tein. This can be, for example, a channel or primary active transporter. Interest- ingly, also accessory factors involved in transport are included. Classes 6 and 7 are currently empty and serve as placeholders for yet undiscovered types of transport and class 9 contains not yet fully characterized transporters. Next, a letter indicates the transporter subclass (e.g., energy source for primary active transport), followed by a number for the transporter family or superfamily. The assignment of a transporter to a specific family follows strict statistical criteria of homology, requiring comparison over a region of at least 60 residues and a prob- ability of 10 19 or less than this degree of sequence similarity occurred by coinci- dence [25]. The fourth level indicates the transporter subfamily and the last level classifies a transport system according to its substrate or range of substrates. To summarize, the first two levels describe the function of the transporter, the next two classify according to phylogenetic similarity, and the last one defines the substrate or indicates the belonging to a transport system. Table 1.2 Transport system 2.A.22.6.3 as an example of the TCDB classification. TCDB level TC number of TCDB name of the exemplary level the level Transporter class (level 1, 2 Electrochemical potential-driven functional): transporters Transporter subclass (level 2, 2.A Porters (uniporters, symporters, and functional): antiporters) Transporter family/superfamily 2.A.22 The neurotransmitter:sodium symporter (level 3, phylogenetic): family Transporter subfamily (level 4, 2.A.22.6 No explicit level name phylogenetic): TCDB level 5 (examples for the 2.A.22.6.3 No explicit level name, given examples: transport system having the Sodium-dependent neutral amino acid same substrate): transporter B(0)AT1 (human) Sodium-dependent neutral amino acid transporter B(0)AT1 (mouse) Transmembrane protein 27
Load more

Recommended publications
  • Iron Transport Proteins: Gateways of Cellular and Systemic Iron Homeostasis
    Iron transport proteins: Gateways of cellular and systemic iron homeostasis Mitchell D. Knutson, PhD University of Florida Essential Vocabulary Fe Heme Membrane Transport DMT1 FLVCR Ferroportin HRG1 Mitoferrin Nramp1 ZIP14 Serum Transport Transferrin Transferrin receptor 1 Cytosolic Transport PCBP1, PCBP2 Timeline of identification in mammalian iron transport Year Protein Original Publications 1947 Transferrin Laurell and Ingelman, Acta Chem Scand 1959 Transferrin receptor 1 Jandl et al., J Clin Invest 1997 DMT1 Gunshin et al., Nature; Fleming et al. Nature Genet. 1999 Nramp1 Barton et al., J Leukocyt Biol 2000 Ferroportin Donovan et al., Nature; McKie et al., Cell; Abboud et al. J. Biol Chem 2004 FLVCR Quigley et al., Cell 2006 Mitoferrin Shaw et al., Nature 2006 ZIP14 Liuzzi et al., Proc Natl Acad Sci USA 2008 PCBP1, PCBP2 Shi et al., Science 2013 HRG1 White et al., Cell Metab DMT1 (SLC11A2) • Divalent metal-ion transporter-1 • Former names: Nramp2, DCT1 Fleming et al. Nat Genet, 1997; Gunshin et al., Nature 1997 • Mediates uptake of Fe2+, Mn2+, Cd2+ • H+ coupled transporter (cotransporter, symporter) • Main roles: • intestinal iron absorption Illing et al. JBC, 2012 • iron assimilation by erythroid cells DMT1 (SLC11A2) Yanatori et al. BMC Cell Biology 2010 • 4 different isoforms: 557 – 590 a.a. (hDMT1) Hubert & Hentze, PNAS, 2002 • Function similarly in iron transport • Differ in tissue/subcellular distribution and regulation • Regulated by iron: transcriptionally (via HIF2α) post-transcriptionally (via IRE) IRE = Iron-Responsive Element Enterocyte Lumen DMT1 Fe2+ Fe2+ Portal blood Enterocyte Lumen DMT1 Fe2+ Fe2+ Fe2+ Fe2+ Ferroportin Portal blood Ferroportin (SLC40A1) • Only known mammalian iron exporter Donovan et al., Nature 2000; McKie et al., Cell 2000; Abboud et al.
    [Show full text]
  • Cystine–Glutamate Antiporter Xct Deficiency Suppresses Tumor Growth While Preserving Antitumor Immunity
    Cystine–glutamate antiporter xCT deficiency suppresses tumor growth while preserving antitumor immunity Michael D. Arensmana, Xiaoran S. Yanga, Danielle M. Leahya, Lourdes Toral-Barzaa, Mary Mileskia, Edward C. Rosfjorda, Fang Wanga, Shibing Dengb, Jeremy S. Myersa, Robert T. Abrahamb, and Christina H. Enga,1 aOncology Research & Development, Pfizer, Pearl River, NY 10965; and bOncology Research & Development, Pfizer, San Diego, CA 92121 Edited by William G. Kaelin Jr., Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, and approved April 2, 2019 (received for review September 1, 2018) T cell-invigorating cancer immunotherapies have near-curative Thus, tumor cells may rely on xCT to fulfill the majority of their potential. However, their clinical benefit is currently limited, as cysteine and GSH needs by importing cystine. only a fraction of patients respond, suggesting that these regimens Inhibition of xCT has been investigated as a therapeutic may benefit from combination with tumor-targeting treatments. As strategy for cancer based on observations that elevated xCT ex- oncogenic progression is accompanied by alterations in metabolic pression on tumor cells correlates with poor prognosis (10–12) pathways, tumors often become heavily reliant on antioxidant and that inhibition of xCT in preclinical studies suppresses tumor machinery and may be susceptible to increases in oxidative stress. growth (10, 12–14). However, these studies relied heavily on the The cystine–glutamate antiporter xCT is frequently overexpressed in use of sulfasalazine, a clinical compound used for the treatment cancer and fuels the production of the antioxidant glutathione; thus, of rheumatoid arthritis, ulcerative colitis, and Crohn’s disease.
    [Show full text]
  • Crystal Structures of the Gastric Proton Pump Reveal the Mechanism for Proton Extrusion
    Life Science Research Frontiers 2018 Research Frontiers 2018 Crystal structures of the gastric proton pump reveal the mechanism for proton extrusion After intaking food, the pH inside our stomach phosphorylation (P), and actuator (A) domains reaches around 1. This acidic environment, (Fig. 2(a)). The β-subunit has a single TM helix and generated by the gastric proton pump H+,K+-ATPase a large ectodomain with three of the six N-linked [1], is indispensable for food digestion and is also glycosylation sites visualized in the structure. The an important barrier to pathogen invasion via the electron density maps define the binding mode of oral route. However, excess stomach acidification vonoprazan (now available for clinical treatment) and induces ulcers, which considerably impair the health SCH28080 (a prototype of P-CAB), and the residues of those affected. Acid suppression in combination coordinating them, in a luminal-facing conduit that with antibiotics is a widely recognized treatment to extends to the cation-binding site (Figs. 2(b) and 2(c)). eradicate Helicobactor pylori, a strong risk factor for The binding sites of these P-CABs were previously gastric cancer. Proton pump inhibitors (PPIs) and a thought to overlap owing to similar inhibitory actions. recently developed class of acid suppressants called Our structures show that they do indeed partially K+-competitive acid blockers (P-CABs) are commonly overlap but are also distinct. The binding mode used for the treatment of acid-related diseases. of P-CABs determined in the crystal structure is Gastric H+,K+-ATPase therefore continues to be a consistent with mutagenesis studies, providing prominent target for the treatment of excess stomach the molecular basis for P-CAB binding to H+,K+- acidification.
    [Show full text]
  • Iron Depletion Reduces Abce1 Transcripts While Inducing The
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 22 October 2019 doi:10.20944/preprints201910.0252.v1 1 Research Article 2 Iron depletion Reduces Abce1 Transcripts While 3 Inducing the Mitophagy Factors Pink1 and Parkin 4 Jana Key 1,2, Nesli Ece Sen 1, Aleksandar Arsovic 1, Stella Krämer 1, Robert Hülse 1, Suzana 5 Gispert-Sanchez 1 and Georg Auburger 1,* 6 1 Experimental Neurology, Goethe University Medical School, 60590 Frankfurt am Main; 7 2 Faculty of Biosciences, Goethe-University Frankfurt am Main, Germany 8 * Correspondence: [email protected] 9 10 Abstract: Lifespan extension was recently achieved in Caenorhabditis elegans nematodes by 11 mitochondrial stress and mitophagy, triggered via iron depletion. Conversely in man, deficient 12 mitophagy due to Pink1/Parkin mutations triggers iron accumulation in patient brain and limits 13 survival. We now aimed to identify murine fibroblast factors, which adapt their mRNA expression 14 to acute iron manipulation, relate to mitochondrial dysfunction and may influence survival. After 15 iron depletion, expression of the plasma membrane receptor Tfrc with its activator Ireb2, the 16 mitochondrial membrane transporter Abcb10, the heme-release factor Pgrmc1, the heme- 17 degradation enzyme Hmox1, the heme-binding cholesterol metabolizer Cyp46a1, as well as the 18 mitophagy regulators Pink1 and Parkin showed a negative correlation to iron levels. After iron 19 overload, these factors did not change expression. Conversely, a positive correlation of mRNA levels 20 with both conditions of iron availability was observed for the endosomal factors Slc11a2 and Steap2, 21 as well as for the iron-sulfur-cluster (ISC)-containing factors Ppat, Bdh2 and Nthl1.
    [Show full text]
  • Primary and Secondary Thyroid Hormone Transporters Anita Kinne, Ralf Schülein, Gerd Krause*
    Kinne et al. Thyroid Research 2011, 4(Suppl 1):S7 http://www.thyroidresearchjournal.com/content/4/S1/S7 REVIEW Open Access Primary and secondary thyroid hormone transporters Anita Kinne, Ralf Schülein, Gerd Krause* Abstract Thyroid hormones (TH) are essential for the development of the human brain, growth and cellular metabolism. Investigation of TH transporters became one of the emerging fields in thyroid research after the discovery of inactivating mutations in the Monocarboxylate transporter 8 (MCT8), which was found to be highly specific for TH transport. However, additional transmembrane transporters are also very important for TH uptake and efflux in different cell types. They transport TH as secondary substrates and include the aromatic amino acid transporting MCT10, the organic anion transporting polypeptides (e.g. OATP1C1, OATP1A2, OPTP1A4) and the large neutral amino acid transporters (LAT1 and LAT2). These TH transporters characteristically possess 12 transmembrane spanners but due to the strong differing sequences between the three transporter families we assume an identical conformation is not very likely. In contrast to the others, the LAT family members form a heterodimer with the escort protein 4F2hc/CD98. A comparison of sequence proportions, locations and types of functional sensitive features for TH transport discovered by mutations, revealed that transport sensitive charged residues occur as conserved amino acids only within each family of the transporter types but not in all putative TH transporters. Based on the lack of highly conserved sensitive charged residues throughout the three transporter families as a common counterpart for the amino acid moiety of the substrates, we conclude that the molecular transport mechanism is likely organized either a) by different molecular determinants in the divergent transporter types or b) the counterparts for the substrates` amino acid moiety at the transporter are not any charged side chains but other proton acceptors or donators.
    [Show full text]
  • ABCG1 (ABC8), the Human Homolog of the Drosophila White Gene, Is a Regulator of Macrophage Cholesterol and Phospholipid Transport
    ABCG1 (ABC8), the human homolog of the Drosophila white gene, is a regulator of macrophage cholesterol and phospholipid transport Jochen Klucken*, Christa Bu¨ chler*, Evelyn Orso´ *, Wolfgang E. Kaminski*, Mustafa Porsch-Ozcu¨ ¨ ru¨ mez*, Gerhard Liebisch*, Michael Kapinsky*, Wendy Diederich*, Wolfgang Drobnik*, Michael Dean†, Rando Allikmets‡, and Gerd Schmitz*§ *Institute for Clinical Chemistry and Laboratory Medicine, University of Regensburg, 93042 Regensburg, Germany; †National Cancer Institute, Laboratory of Genomic Diversity, Frederick, MD 21702-1201; and ‡Departments of Ophthalmology and Pathology, Columbia University, Eye Research Addition, New York, NY 10032 Edited by Jan L. Breslow, The Rockefeller University, New York, NY, and approved November 3, 1999 (received for review June 14, 1999) Excessive uptake of atherogenic lipoproteins such as modified low- lesterol transport. Although several effector molecules have been density lipoprotein complexes by vascular macrophages leads to proposed to participate in macrophage cholesterol efflux (6, 9), foam cell formation, a critical step in atherogenesis. Cholesterol efflux including endogenous apolipoprotein E (10) and the cholesteryl mediated by high-density lipoproteins (HDL) constitutes a protective ester transfer protein (11), the detailed molecular mechanisms mechanism against macrophage lipid overloading. The molecular underlying cholesterol export in these cells have not yet been mechanisms underlying this reverse cholesterol transport process are characterized. currently not fully understood. To identify effector proteins that are Recently, mutations of the ATP-binding cassette (ABC) trans- involved in macrophage lipid uptake and release, we searched for porter ABCA1 gene have been causatively linked to familial HDL genes that are regulated during lipid influx and efflux in human deficiency and Tangier disease (12–14).
    [Show full text]
  • Effects of Silencing the ATP-Binding Cassette Protein E1 Gene by Electroporation on the Proliferation and Migration of EC109 Human Esophageal Cancer Cells
    MOLECULAR MEDICINE REPORTS 12: 837-842, 2015 Effects of silencing the ATP-binding cassette protein E1 gene by electroporation on the proliferation and migration of EC109 human esophageal cancer cells XIAO-RUI LI, LIU-ZHONG YANG, XIAO-QING HUO, YING WANG, QING-HUI YANG and QING-QIN ZHANG Department of Oncology, The First Affiliated Hospital of Xinxiang Medical College, Weihui, Henan 453100, P.R. China Received February 17, 2014; Accepted November 19, 2014 DOI: 10.3892/mmr.2015.3512 Abstract. In the present study, the gene expression of invasion and migration in esophageal cancer and silencing the ATP-binding cassette protein E1 (ABCE1) in the EC109 ABCE1 gene by electroporation can significantly reduce the human esophageal cancer cell line was silenced using elec- proliferation, invasion and migration capacity of EC109 cells troporation to examine the effect if the ABCE1 gene on the in vitro. growth migration and cell cycle of cancer cells. The small interference (si)RNA sequence of ABCE1 was designed and Introduction synthesized to transfect the EC109 cells by electroporation. The mRNA and protein expression levels of ABCE1 were Esophageal cancer is one of most common types of gastro- then detected by reverse transcription quantitative polymerase intestinal malignant tumor in humans. The incidence of the chain reaction (RT-qPCR) and western blot analysis. The disease is higher in developing countries and the majority of analysis of the cell cycle and apoptosis was performed using tumors are squamous carcinoma (1). Although chemotherapy flow cytometry. The effect of silencing the ABCE1 gene on and adjuvant chemotherapy are widely used the treatment of the proliferation, migration and invasive ability of the EC109 esophageal cancer, the prognosis remains poor, particularly human esophageal cancer cells were assessed using a Cell in patients with clinical migration and tumor recurrence (2,3).
    [Show full text]
  • Alternating Hypoglycemia and Hyperglycemia in a Toddler with a Homozygous P.R1419H ABCC8 Mutation: an Unusual Clinical Picture
    J Pediatr Endocr Met 2015; 28(3-4): 345–351 Patient report Open Access Shira Harel, Ana S.A. Cohen, Khalid Hussain, Sarah E. Flanagan, Kamilla Schlade-Bartusiak, Millan Patel, Jaques Courtade, Jenny B.W. Li, Clara Van Karnebeek, Harley Kurata, Sian Ellard, Jean-Pierre Chanoine and William T. Gibson* Alternating hypoglycemia and hyperglycemia in a toddler with a homozygous p.R1419H ABCC8 mutation: an unusual clinical picture Abstract Results: A 16-month-old girl of consanguineous descent manifested hypoglycemia. She had dysregulation of Background: Inheritance of two pathogenic ABCC8 alleles insulin secretion, with postprandial hyperglycemia fol- typically causes severe congenital hyperinsulinism. We lowed by hypoglycemia. Microarray revealed homozygo- describe a girl and her father, both homozygous for the sity for the regions encompassing KCNJ11 and ABCC8. Her same ABCC8 mutation, who presented with unusual father had developed diabetes at 28 years of age. Sequenc- phenotypes. ing of ABCC8 identified a homozygous missense mutation, Methods: Single nucleotide polymorphism microarray p.R1419H, in both individuals. Functional studies showed and Sanger sequencing were performed. Western blot, absence of working KATP channels. rubidium efflux, and patch clamp recordings interrogated Conclusion: This is the first description of a homozygous the expression and activity of the mutant protein. p.R1419H mutation. Our findings highlight that homozy- gous loss-of-function mutations of ABCC8 do not neces- sarily translate into early-onset severe hyperinsulinemia. *Corresponding author: William T. Gibson, Child and Family Research Institute, Department of Medical Genetics, British Keywords: ABCC8; diabetes; hyperglycemia; hyperinsu- Columbia Children’s Hospital, 950 West 28th Avenue, Vancouver, linism; hypoglycemia. BC, V5Z 4H4, Canada, Phone: +1-604-875-2000 ext.
    [Show full text]
  • A Comprehensive Mapping of the Structure and Gene Organisation in the Sheep MHC Class I Region N
    Siva Subramaniam et al. BMC Genomics (2015) 16:810 DOI 10.1186/s12864-015-1992-4 RESEARCH ARTICLE Open Access A comprehensive mapping of the structure and gene organisation in the sheep MHC class I region N. Siva Subramaniam1, EF Morgan1, JD Wetherall1, MJ Stear2,3* and DM Groth1 Abstract Background: The major histocompatibility complex (MHC) is a chromosomal region that regulates immune responsiveness in vertebrates. This region is one of the most important for disease resistance because it has been associated with resistance or susceptibility to a wide variety of diseases and because the MHC often accounts for more of the variance than other loci. Selective breeding for disease resistance is becoming increasingly common in livestock industries, and it is important to determine how this will influence MHC polymorphism and resistance to diseases that are not targeted for selection. However, in sheep the order and sequence of the protein coding genes is controversial. Yet this information is needed to determine precisely how the MHC influences resistance and susceptibility to disease. Methods: CHORI bacterial artificial chromosomes (BACs) known to contain sequences from the sheep MHC class I region were sub-cloned, and the clones partially sequenced. The resulting sequences were analysed and re-assembled to identify gene content and organisation within each BAC. The low resolution MHC class I physical map was then compared to the cattle reference genome, the Chinese Merino sheep MHC map published by Gao, et al. (2010) and the recently available sheep reference genome. Results: Immune related class I genes are clustered into 3 blocks; beta, kappa and a novel block not previously identified in other organisms.
    [Show full text]
  • Variable Priming of a Docked Synaptic Vesicle PNAS PLUS
    Variable priming of a docked synaptic vesicle PNAS PLUS Jae Hoon Junga,b,c, Joseph A. Szulea,c, Robert M. Marshalla,c, and Uel J. McMahana,c,1 aDepartment of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305; bDepartment of Physics, Stanford University School of Humanities and Sciences, Stanford, CA 94305; and cDepartment of Biology, Texas A&M University, College Station, TX 77845 Edited by Thomas S. Reese, National Institutes of Health, Bethesda, MD, and approved January 12, 2016 (received for review November 30, 2015) The priming of a docked synaptic vesicle determines the proba- transition. Biochemical and electrophysiological approaches have bility of its membrane (VM) fusing with the presynaptic membrane provided evidence that priming is mediated by interactions be- (PM) when a nerve impulse arrives. To gain insight into the nature tween the SNARE proteins and their regulators (7, 12–14, 24) and of priming, we searched by electron tomography for structural can involve differences in positioning of docked SVs relative to + relationships correlated with fusion probability at active zones of Ca2 channels (25). Biochemistry has also led to the suggestion axon terminals at frog neuromuscular junctions. For terminals that primed SVs may become deprimed (26). fixed at rest, the contact area between the VM of docked vesicles We have previously shown by electron tomography on frog and PM varied >10-fold with a normal distribution. There was no neuromuscular junctions (NMJs) fixed at rest that there are, for merging of the membranes. For terminals fixed during repetitive docked SVs, variations in the extent of the VM–PM contact area evoked synaptic transmission, the normal distribution of contact and in the length of the several AZM macromolecules linking areas was shifted to the left, due in part to a decreased number of the VM to the PM, the so-called ribs, pegs, and pins (2, 27).
    [Show full text]
  • A Model of Mitochonrial Calcium Induced Calcium
    A MODEL OF MITOCHONRIAL CALCIUM INDUCED CALCIUM RELEASE DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Balbir Thomas, The Ohio State University 2007 Dissertation Committee: Approved by David Terman, Adviser Douglas R. Pfeiffer Adviser Edward Overman Biophysics Graduate Program Christopher P. Fall ABSTRACT Cytoplasmic calcium plays a dual role in cellular physiology. On one hand it acts as a second messenger in intra-cellular signalling, and on the other hand it is also the trigger for calcium dependent apopotosis. A mechanistic explanation of this dual role of cytoplasmic calcium was proposed by Ichas and Mazat. Their hypothesis involved the permeability transition pore was based on the observation that the permeability transition pore can exist in multiple conductance states. Specifically there exist a persistent high conductance state and a transitory low conductance state. Ichas et.al. also observed that the low conductance state is opened by a rise in mitochondrial matrix pH, in contrast to what was already know about the high conductance state, which opens in response to prolonged elevation of mitochondrial calcium. In this dissertation we build a detailed, physiological model of the mitochondrial switch between calcium signalling and cell death based on a simple three state model of the permeability transition pore. This model agrees with the substance of the Ichas and Mazat hypothesis and provides a substrate for further modeling to study the spatial and temporal dynamics of mitochondrial involvement in intracellular calcium signalling, and the interaction of mitochondria and endoplasmic reticulum during this process.
    [Show full text]
  • Transport of Sugars
    BI84CH32-Frommer ARI 29 April 2015 12:34 Transport of Sugars Li-Qing Chen,1,∗ Lily S. Cheung,1,∗ Liang Feng,3 Widmar Tanner,2 and Wolf B. Frommer1 1Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305; email: [email protected] 2Zellbiologie und Pflanzenbiochemie, Universitat¨ Regensburg, 93040 Regensburg, Germany 3Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305 Annu. Rev. Biochem. 2015. 84:865–94 Keywords First published online as a Review in Advance on glucose, sucrose, carrier, GLUT, SGLT, SWEET March 5, 2015 The Annual Review of Biochemistry is online at Abstract biochem.annualreviews.org Soluble sugars serve five main purposes in multicellular organisms: as sources This article’s doi: of carbon skeletons, osmolytes, signals, and transient energy storage and as 10.1146/annurev-biochem-060614-033904 transport molecules. Most sugars are derived from photosynthetic organ- Copyright c 2015 by Annual Reviews. isms, particularly plants. In multicellular organisms, some cells specialize All rights reserved in providing sugars to other cells (e.g., intestinal and liver cells in animals, ∗ These authors contributed equally to this review. photosynthetic cells in plants), whereas others depend completely on an ex- Annu. Rev. Biochem. 2015.84:865-894. Downloaded from www.annualreviews.org ternal supply (e.g., brain cells, roots and seeds). This cellular exchange of Access provided by b-on: Universidade de Lisboa (UL) on 09/05/16. For personal use only. sugars requires transport proteins to mediate uptake or release from cells or subcellular compartments. Thus, not surprisingly, sugar transport is criti- cal for plants, animals, and humans.
    [Show full text]